DNA Barcoding of Israeli Indigenous and Introduced Cichlids

The objectives of this study were barcoding and taxonomic analysis of the five tilapiine species (Oreochromis aureus, O. niloticus, O. mossam- bicus, Sarotherodon galilaeus, and Tilapia zillii), two tilapia hybrid strains (Florida red tilapia and Philippine red tilapia), and two endemic wild cichlids (Tristramella simonis and Astatotilapia flaviijosephi) available in Israel, as well as O. urolepis hornorum. Cytochrome oxidase subunit I (COI) 619 bp sequence traces of 104 individuals were assembled, aligned, and compared (GenBank project GI 209553463). The DNA sequences of two hybrid strains were identical to those of O. hornorum and O. aureus. Absence of intra-specific variability was detected in the commercially used species, O. aureus, S. galilaeus, O. mossambicus, and O. urolepis horno- rum. Two DNA sequence variants were detected in O. niloticus originating from Ghana and Egypt. In contrast, 2-3 variants were detected in the DNA of each of the non-commercial species. Amino-acid sequences were identical in all “true tilapias” and different from the sequences in the endemic cichlids. As a whole, the protein phylogenetic tree fitted the expected conventional taxonomy as opposed to the respective DNA-based tree. Sequences FJ348047-FJ348150 were submitted to GenBank via the BOLD database (identical to FISH001-08 - FISH104-08 in this database)

Efficient Inference of Haplotypes From Genotypes on a Large Animal Pedigree

We present a simple algorithm for reconstruction of haplotypes from a sample of multilocus genotypes. The algorithm is aimed specifically for analysis of very large pedigrees for small chromosomal segments, where recombination frequency within the chromosomal segment can be assumed to be zero. The algorithm was tested both on simulated pedigrees of 155 individuals in a family structure of three generations and on real data of 1149 animals from the Israeli Holstein dairy cattle population, including 406 bulls with genotypes, but no females with genotypes. The rate of haplotype resolution for the simulated data was >91% with a standard deviation of 2%. With 20% missing data, the rate of haplotype resolution was 67.5% with a standard deviation of 1.3%. In both cases all recovered haplotypes were correct. In the real data, allele origin was resolved for 22% of the heterozygous genotypes, even though 70% of the genotypes were missing. Haplotypes were resolved for 36% of the males. Computing time was insignificant for both data sets. Despite the intricacy of large-scale real pedigree genotypes, the proposed algorithm provides a practical rule-based solution for resolving haplotypes for small chromosomal segments in commercial animal populations

Identification of a missense mutation in the bovine ABCG2 gene with a major effect on the QTL on chromosome 6 affecting milk yield and composition in Holstein cattle

We previously localized a quantitative trait locus (QTL) on chromosome 6 affecting milk fat and protein concentration to a 4-cM confidence interval, centered on the microsatellite BM143. We characterized the genes and sequence variation in this region and identified common haplotypes spanning five polymorphic sites in the genes IBSP, SPP1, PKD2, and ABCG2 for two sires heterozygous for this QTL. Expression of SPP1 and ABCG2 in the bovine mammary gland increased from parturition through lactation. SPP1 and all the coding exons of ABCG2 and PKD2 were sequenced for these two sires. The single nucleotide change capable of encoding a substitution of tyrosine-581 to serine (Y581S) in the ABCG2 transporter was the only polymorphism corresponding to the segregation status of all 3 heterozygous and 15 homozygous sires for the QTL in the Israeli and U.S. Holstein populations. The allele substitution fixed effects on the genetic evaluations of 335 Israeli sires were –341 kg milk, +0.16% fat, and +0.13% protein (F-value = 200). No other polymorphism gave significant effect for fat and protein concentration in models that also included Y581S. The allele substitution effects on the genetic evaluations of 670 cows, daughters of two heterozygous sires, were –226 kg milk, 0.09% fat, and 0.08% protein (F-value = 394), with partial dominance towards the 581S homozygotes. We therefore propose that Y581S in ABCG2 is the causative site for this QTL

Whole-genome resequencing of two elite sires for the detection of haplotypes under selection in dairy cattle

Using a combination of whole-genome resequencing and high-density genotyping arrays, genome-wide haplotypes were reconstructed for two of the most important bulls in the history of the dairy cattle industry, Pawnee Farm Arlinda Chief (“Chief”) and his son Walkway Chief Mark (“Mark”), each accounting for ∼7% of all current genomes. We aligned 20.5 Gbp (∼7.3× coverage) and 37.9 Gbp (∼13.5× coverage) of the Chief and Mark genomic sequences, respectively. More than 1.3 million high-quality SNPs were detected in Chief and Mark sequences. The genome-wide haplotypes inherited by Mark from Chief were reconstructed using ∼1 million informative SNPs. Comparison of a set of 15,826 SNPs that overlapped in the sequence-based and BovineSNP50 SNPs showed the accuracy of the sequence-based haplotype reconstruction to be as high as 97%. By using the BovineSNP50 genotypes, the frequencies of Chief alleles on his two haplotypes then were determined in 1,149 of his descendants, and the distribution was compared with the frequencies that would be expected assuming no selection. We identified 49 chromosomal segments in which Chief alleles showed strong evidence of selection. Candidate polymorphisms for traits that have been under selection in the dairy cattle population then were identified by referencing Chief’s DNA sequence within these selected chromosome blocks. Eleven candidate genes were identified with functions related to milk-production, fertility, and disease-resistance traits. These data demonstrate that haplotype reconstruction of an ancestral proband by whole-genome resequencing in combination with high-density SNP genotyping of descendants can be used for rapid, genome-wide identification of the ancestor’s alleles that have been subjected to artificial selection